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Spurgin LG, Bosse M, Adriaensen F, Albayrak T, Barboutis C, Belda E, Bushuev A, Cecere JG, Charmantier A, Cichon M, Dingemanse NJ, Doligez B, Eeva T, Erikstad KE, Fedorov V, Griggio M, Heylen D, Hille S, Hinde CA, Ivankina E, Kempenaers B, Kerimov A, Krist M, Kvist L, Laine VN, Mänd R, Matthysen E, Nager R, Nikolov BP, Norte AC, Orell M, Ouyang J, Petrova-Dinkova G, Richner H, Rubolini D, Slagsvold T, Tilgar V, Török J, Tschirren B, Vágási CI, Yuta T, Groenen MAM, Visser ME, van Oers K, Sheldon BC, Slate J. The great tit HapMap project: A continental-scale analysis of genomic variation in a songbird. Mol Ecol Resour 2024; 24:e13969. [PMID: 38747336 DOI: 10.1111/1755-0998.13969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/10/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024]
Abstract
A major aim of evolutionary biology is to understand why patterns of genomic diversity vary within taxa and space. Large-scale genomic studies of widespread species are useful for studying how environment and demography shape patterns of genomic divergence. Here, we describe one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning ~30 degrees of latitude and 40 degrees of longitude - almost the entire geographical range of the European subspecies. Genome-wide variation was consistent with a recent colonisation across Europe from a South-East European refugium, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear 'islands of differentiation', even among populations with very low levels of genome-wide differentiation. Low local recombination rates were a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination causes highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, probably as a result of recent directional selection at the species' range edges. Haplotype-based measures of selection were related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into spatio-temporal evolutionary dynamics.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Mirte Bosse
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Department of Ecological Science, Animal Ecology Group, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank Adriaensen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Tamer Albayrak
- Department of Biology, Science and art Faculty, Mehmet Akif Ersoy University, Istiklal Yerleskesi, Burdur, Turkey
- Biology Education, Buca Faculty of Education, Mathematics and Science Education, Dokuz Eylül University, İzmir, Turkey
| | | | - Eduardo Belda
- Institut d'Investigació per a la Gestió Integrada de Zones Costaneres, Campus de Gandia, Universitat Politècnica de València, València, Spain
| | - Andrey Bushuev
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, Italy
| | | | - Mariusz Cichon
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | - Niels J Dingemanse
- Behavioural Ecology, Faculty of Biology, LMU München, Planegg-Martinsried, Germany
| | - Blandine Doligez
- UMR CNRS 5558-LBBE, Biométrie et Biologie Évolutive, Villeurbanne, France
- Department of Ecology and Evolution, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tapio Eeva
- Department of Biology, University of Turku, Turku, Finland
| | - Kjell Einar Erikstad
- Norwegian Institute for Nature Research, FRAM-High North Research Centre for Climate and the Environment, Tromsø, Norway
| | | | - Matteo Griggio
- Department of Biology, University of Padova, Padova, Italy
| | - Dieter Heylen
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Sabine Hille
- Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Science, Vienna, Austria
| | - Camilla A Hinde
- Behavioural Ecology Group, Department of Life Sciences, Anglia Ruskin University, Cambridgeshire, UK
| | - Elena Ivankina
- Faculty of Biology, Zvenigorod Biological Station, Lomonosov Moscow State University, Moscow, Russia
| | - Bart Kempenaers
- Department of Ornithology, Max Planck Institute for Biological Intelligence, Seewiesen, Germany
| | - Anvar Kerimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Milos Krist
- Department of Zoology, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Veronika N Laine
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Raivo Mänd
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Ruedi Nager
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Boris P Nikolov
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ana Claudia Norte
- MARE - Marine and Environmental Sciences Centre, Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Markku Orell
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | | | - Gergana Petrova-Dinkova
- Bulgarian Ornithological Centre, Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Heinz Richner
- Evolutionary Ecology Lab, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università Degli Studi di Milano, Milan, Italy
| | - Tore Slagsvold
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Vallo Tilgar
- Department of Zoology, University of Tartu, Tartu, Estonia
| | - János Török
- Behavioural Ecology Group, Department of Systematic Zoology and Ecology, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Barbara Tschirren
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Csongor I Vágási
- Evolutionary Ecology Group, Hungarian Department of Biology and Ecology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Teru Yuta
- Yamashina Institute for Ornithology, Abiko, Japan
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, the Netherlands
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Ben C Sheldon
- Department of Biology, Edward Grey Institute, University of Oxford, Oxford, UK
| | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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2
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Martin CA, Sheppard EC, Ali HAA, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci? Mol Ecol 2024; 33:e17365. [PMID: 38733214 DOI: 10.1111/mec.17365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 03/01/2024] [Indexed: 05/13/2024]
Abstract
When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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3
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Nosil P, de Carvalho CF, Villoutreix R, Zamorano LS, Sinclair-Waters M, Planidin NP, Parchman TL, Feder J, Gompert Z. Evolution repeats itself in replicate long-term studies in the wild. SCIENCE ADVANCES 2024; 10:eadl3149. [PMID: 38787954 PMCID: PMC11122682 DOI: 10.1126/sciadv.adl3149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/22/2024] [Indexed: 05/26/2024]
Abstract
The extent to which evolution is repeatable remains debated. Here, we study changes over time in the frequency of cryptic color-pattern morphs in 10 replicate long-term field studies of a stick insect, each spanning at least a decade (across 30 years of total data). We find predictable "up-and-down" fluctuations in stripe frequency in all populations, representing repeatable evolutionary dynamics based on standing genetic variation. A field experiment demonstrates that these fluctuations involve negative frequency-dependent natural selection (NFDS). These fluctuations rely on demographic and selective variability that pushes populations away from equilibrium, such that they can reliably move back toward it via NFDS. Last, we show that the origin of new cryptic forms is associated with multiple structural genomic variants such that which mutations arise affects evolution at larger temporal scales. Thus, evolution from existing variation is predictable and repeatable, but mutation adds complexity even for traits evolving deterministically under natural selection.
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Affiliation(s)
- Patrik Nosil
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Laura S. Zamorano
- Theoretical and Experimental Ecology (SETE), CNRS, 2 route du CNRS, 09200 Moulis, France
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | | | - Jeffrey Feder
- Department of Biology, Notre Dame University, South Bend, IN 11111, USA
| | - Zach Gompert
- Department of Biology, Utah State University, Logan, UT 84322, USA
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4
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Vellnow N, Gossmann TI, Waxman D. The pseudoentropy of allele frequency trajectories, the persistence of variation, and the effective population size. Biosystems 2024; 238:105176. [PMID: 38479654 DOI: 10.1016/j.biosystems.2024.105176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
To concisely describe how genetic variation, at individual loci or across whole genomes, changes over time, and to follow transitory allelic changes, we introduce a quantity related to entropy, that we term pseudoentropy. This quantity emerges in a diffusion analysis of the mean time a mutation segregates in a population. For a neutral locus with an arbitrary number of alleles, the mean time of segregation is generally proportional to the pseudoentropy of initial allele frequencies. After the initial time point, pseudoentropy generally decreases, but other behaviours are possible, depending on the genetic diversity and selective forces present. For a biallelic locus, pseudoentropy and entropy coincide, but they are distinct quantities with more than two alleles. Thus for populations with multiple biallelic loci, the language of entropy suffices. Then entropy, combined across loci, serves as a concise description of genetic variation. We used individual based simulations to explore how this entropy behaves under different evolutionary scenarios. In agreement with predictions, the entropy associated with unlinked neutral loci decreases over time. However, deviations from free recombination and neutrality have clear and informative effects on the entropy's behaviour over time. Analysis of publicly available data of a natural D. melanogaster population, that had been sampled over seven years, using a sliding-window approach, yielded considerable variation in entropy trajectories of different genomic regions. These mostly follow a pattern that suggests a substantial effective population size and a limited effect of positive selection on genome-wide diversity over short time scales.
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Affiliation(s)
- Nikolas Vellnow
- TU Dortmund University, Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, Emil-Figge-Str. 66, 44227 Dortmund, Germany.
| | - Toni I Gossmann
- TU Dortmund University, Computational Systems Biology, Faculty of Biochemical and Chemical Engineering, Emil-Figge-Str. 66, 44227 Dortmund, Germany.
| | - David Waxman
- Fudan University, Centre for Computational Systems Biology, ISTBI, 220 Handan Road, Shanghai 200433, People's Republic of China.
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5
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Cheng Y, Lei F. Avian lower beak is always overlooked: its coordinate role in shaping species-specific beak should not be underestimated. Integr Zool 2024; 19:339-342. [PMID: 37794566 DOI: 10.1111/1749-4877.12769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Affiliation(s)
- Yalin Cheng
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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6
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Mirchandani CD, Shultz AJ, Thomas GWC, Smith SJ, Baylis M, Arnold B, Corbett-Detig R, Enbody E, Sackton TB. A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics. Mol Biol Evol 2024; 41:msad270. [PMID: 38069903 PMCID: PMC10764099 DOI: 10.1093/molbev/msad270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.
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Affiliation(s)
- Cade D Mirchandani
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Allison J Shultz
- Ornithology Department, Natural History Museum of Los Angeles County, Los Angeles, CA 90007, USA
| | | | - Sara J Smith
- Informatics Group, Harvard University, Cambridge, MA, USA
- Biology, Mount Royal University, Calgary, AB T3E 6K6, Canada
| | - Mara Baylis
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Brian Arnold
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Center for Statistics and Machine Learning, Princeton University, Princeton, NJ, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik Enbody
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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7
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Zichello JM, DeLiberto ST, Holmes P, Pierwola AA, Werner SJ. Recent beak evolution in North American starlings after invasion. Sci Rep 2024; 14:140. [PMID: 38167426 PMCID: PMC10761893 DOI: 10.1038/s41598-023-49623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
European starlings are one of the most abundant and problematic avian invaders in the world. From their native range across Eurasia and North Africa, they have been introduced to every continent except Antarctica. In 160 years, starlings have expanded into different environments throughout the world, making them a powerful model for understanding rapid evolutionary change and adaptive plasticity. Here, we investigate their spatiotemporal morphological variation in North America and the native range. Our dataset includes 1217 specimens; a combination of historical museum skins and modern birds. Beak length in the native range has remained unchanged during the past 206 years, but we find beak length in North American birds is now 8% longer than birds from the native range. We discuss potential drivers of this pattern including dietary adaptation or climatic pressures. Additionally, body size in North American starlings is smaller than those from the native range, which suggests a role for selection or founder effect. Taken together, our results indicate rapid recent evolutionary change in starling morphology coincident with invasion into novel environments.
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Affiliation(s)
- Julia M Zichello
- Hunter College, City University of New York, New York, NY, USA.
- Division of Anthropology, American Museum of Natural History, New York, NY, USA.
| | - Shelagh T DeLiberto
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
| | - Paul Holmes
- Animal and Plant Health Agency, Shrewsbury Veterinary Investigation Centre, Shrewsbury, SY1 4HD, UK
| | - Agnieszka A Pierwola
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Scott J Werner
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, USA
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Knutie SA, Webster CN, Vaziri GJ, Albert L, Harvey JA, LaRue M, Verrett TB, Soldo A, Koop JAH, Chaves JA, Wegrzyn JL. Urban living can rescue Darwin's finches from the lethal effects of invasive vampire flies. GLOBAL CHANGE BIOLOGY 2024; 30:e17145. [PMID: 38273516 DOI: 10.1111/gcb.17145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Human activity changes multiple factors in the environment, which can have positive or negative synergistic effects on organisms. However, few studies have explored the causal effects of multiple anthropogenic factors, such as urbanization and invasive species, on animals and the mechanisms that mediate these interactions. This study examines the influence of urbanization on the detrimental effect of invasive avian vampire flies (Philornis downsi) on endemic Darwin's finches in the Galápagos Islands. We experimentally manipulated nest fly abundance in urban and non-urban locations and then characterized nestling health, fledging success, diet, and gene expression patterns related to host defense. Fledging success of non-parasitized nestlings from urban (79%) and non-urban (75%) nests did not differ significantly. However, parasitized, non-urban nestlings lost more blood, and fewer nestlings survived (8%) compared to urban nestlings (50%). Stable isotopic values (δ15 N) from urban nestling feces were higher than those from non-urban nestlings, suggesting that urban nestlings are consuming more protein. δ15 N values correlated negatively with parasite abundance, which suggests that diet might influence host defenses (e.g., tolerance and resistance). Parasitized, urban nestlings differentially expressed genes within pathways associated with red blood cell production (tolerance) and pro-inflammatory response (innate immunological resistance), compared to parasitized, non-urban nestlings. In contrast, parasitized non-urban nestlings differentially expressed genes within pathways associated with immunoglobulin production (adaptive immunological resistance). Our results suggest that urban nestlings are investing more in pro-inflammatory responses to resist parasites but also recovering more blood cells to tolerate blood loss. Although non-urban nestlings are mounting an adaptive immune response, it is likely a last effort by the immune system rather than an effective defense against avian vampire flies since few nestlings survived.
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Affiliation(s)
- Sarah A Knutie
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
| | - Cynthia N Webster
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Grace J Vaziri
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Lauren Albert
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Johanna A Harvey
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Department of Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Michelle LaRue
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | - Taylor B Verrett
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Alexandria Soldo
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer A H Koop
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, USA
| | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, California, USA
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
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9
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Mascarenhas R, Meirelles PM, Batalha-Filho H. Urbanization drives adaptive evolution in a Neotropical bird. Curr Zool 2023; 69:607-619. [PMID: 37637315 PMCID: PMC10449428 DOI: 10.1093/cz/zoac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023] Open
Abstract
Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.
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Affiliation(s)
- Rilquer Mascarenhas
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Pedro Milet Meirelles
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
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10
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Taylor RS. New tools for the recovery of the kākāpō. Nat Ecol Evol 2023; 7:1589-1590. [PMID: 37640764 DOI: 10.1038/s41559-023-02112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology Division, Environment and Climate Change Canada, Ottawa, Ontario, Canada.
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11
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Guhlin J, Le Lec MF, Wold J, Koot E, Winter D, Biggs PJ, Galla SJ, Urban L, Foster Y, Cox MP, Digby A, Uddstrom LR, Eason D, Vercoe D, Davis T, Howard JT, Jarvis ED, Robertson FE, Robertson BC, Gemmell NJ, Steeves TE, Santure AW, Dearden PK. Species-wide genomics of kākāpō provides tools to accelerate recovery. Nat Ecol Evol 2023; 7:1693-1705. [PMID: 37640765 DOI: 10.1038/s41559-023-02165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 07/11/2023] [Indexed: 08/31/2023]
Abstract
The kākāpō is a critically endangered, intensively managed, long-lived nocturnal parrot endemic to Aotearoa New Zealand. We generated and analysed whole-genome sequence data for nearly all individuals living in early 2018 (169 individuals) to generate a high-quality species-wide genetic variant callset. We leverage extensive long-term metadata to quantify genome-wide diversity of the species over time and present new approaches using probabilistic programming, combined with a phenotype dataset spanning five decades, to disentangle phenotypic variance into environmental and genetic effects while quantifying uncertainty in small populations. We find associations for growth, disease susceptibility, clutch size and egg fertility within genic regions previously shown to influence these traits in other species. Finally, we generate breeding values to predict phenotype and illustrate that active management over the past 45 years has maintained both genome-wide diversity and diversity in breeding values and, hence, evolutionary potential. We provide new pathways for informing future conservation management decisions for kākāpō, including prioritizing individuals for translocation and monitoring individuals with poor growth or high disease risk. Overall, by explicitly addressing the challenge of the small sample size, we provide a template for the inclusion of genomic data that will be transformational for species recovery efforts around the globe.
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Affiliation(s)
- Joseph Guhlin
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Marissa F Le Lec
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North, Aotearoa New Zealand
| | - David Winter
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
| | - Patrick J Biggs
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- School of Veterinary Science, Massey University, Palmerston North, Aotearoa New Zealand
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Lara Urban
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
- Helmholtz Pioneer Campus, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Helmholtz AI, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Yasmin Foster
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Murray P Cox
- School of Natural Sciences, Massey University, Palmerston North, Aotearoa New Zealand
- Department of Statistics, University of Auckland, Auckland, Aotearoa New Zealand
| | - Andrew Digby
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Lydia R Uddstrom
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Daryl Eason
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Deidre Vercoe
- Kākāpō Recovery Programme, Department of Conservation, Invercargill, Aotearoa New Zealand
| | - Tāne Davis
- Rakiura Tītī Islands Administering Body, Invercargill, Aotearoa New Zealand
| | - Jason T Howard
- Neurogenetics of Language Lab, The Rockefeller University, New York, NY, USA
- Mirxes, Cambridge, MA, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Fiona E Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Bruce C Robertson
- Department of Zoology, University of Otago, Dunedin, Aotearoa New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, Aotearoa New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, Aotearoa New Zealand
| | - Peter K Dearden
- Genomics Aotearoa, Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, Aotearoa New Zealand.
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12
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Enbody ED, Sendell-Price AT, Sprehn CG, Rubin CJ, Visscher PM, Grant BR, Grant PR, Andersson L. Community-wide genome sequencing reveals 30 years of Darwin's finch evolution. Science 2023; 381:eadf6218. [PMID: 37769091 DOI: 10.1126/science.adf6218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/22/2023] [Indexed: 09/30/2023]
Abstract
A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Ashley T Sendell-Price
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Rd., St. Lucia QLD 4072, Australia
| | - B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, 402 Raymond Stotzer Pkwy Building 2, College Station, TX 77843, USA
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13
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Recuerda M, Palacios M, Frías O, Hobson K, Nabholz B, Blanco G, Milá B. Adaptive phenotypic and genomic divergence in the common chaffinch (Fringilla coelebs) following niche expansion within a small oceanic island. J Evol Biol 2023; 36:1226-1241. [PMID: 37485603 DOI: 10.1111/jeb.14200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023]
Abstract
According to models of ecological speciation, adaptation to adjacent, contrasting habitat types can lead to population divergence given strong enough environment-driven selection to counteract the homogenizing effect of gene flow. We tested this hypothesis in the common chaffinch (Fringilla coelebs) on the small island of La Palma, Canary Islands, where it occupies two markedly different habitats. Isotopic (δ13 C, δ15 N) analysis of feathers indicated that birds in the two habitats differed in ecosystem and/or diet, and analysis of phenotypic traits revealed significant differences in morphology and plumage colouration that are consistent with ecomorphological and ecogeographical predictions respectively. A genome-wide survey of single-nucleotide polymorphism revealed marked neutral structure that was consistent with geography and isolation by distance, suggesting low dispersal. In contrast, loci putatively under selection identified through genome-wide association and genotype-environment association analyses, revealed amarked adaptive divergence between birds in both habitats. Loci associated with phenotypic and environmental differences among habitats were distributed across the genome, as expected for polygenic traits involved in local adaptation. Our results suggest a strong role for habitat-driven local adaptation in population divergence in the chaffinches of La Palma, a process that appears to be facilitated by a strong reduction in effective dispersal distances despite the birds' high dispersal capacity.
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Affiliation(s)
- María Recuerda
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Mercè Palacios
- Department of Biodiversity, Ecology and Evolution, Universidad Complutense de Madrid, Madrid, Spain
| | - Oscar Frías
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Keith Hobson
- Biology Department, Western University, London, Ontario, Canada
| | - Benoit Nabholz
- Institut des Sciences de l'Évolution de Montpellier (ISEM), CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Guillermo Blanco
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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14
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Zheng S, Hu J, Ma Z, Lindenmayer D, Liu J. Increases in intraspecific body size variation are common among North American mammals and birds between 1880 and 2020. Nat Ecol Evol 2023; 7:347-354. [PMID: 36690729 DOI: 10.1038/s41559-022-01967-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/29/2022] [Indexed: 01/24/2023]
Abstract
Many studies have documented the average body size of animals declining over time. Compared to mean body size, less is known about long-term changes in intraspecific trait variation (ITV), which is also important to understanding species' ability to cope with environmental challenges. On the basis of 393,499 specimen records from 380 species collected in North America between 1880 and 2020, we found that body size ITV increased by 9.59% for mammals (n = 302) and 30.67% for birds (n = 78); human-harvested species had higher probability of ITV increase. The observed increasing ITV in many species suggests possible niche expansion and potential buffering effects against downsizing but it risks increased maladaptation to rapidly changing environments. The results demonstrate that trait mean and variance do not necessarily respond in similar ways to anthropogenic pressures and both should be considered.
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Affiliation(s)
- Shilu Zheng
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, School of Life Sciences, Fudan University, Shanghai, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhijun Ma
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, School of Life Sciences, Fudan University, Shanghai, China
| | - David Lindenmayer
- Fenner School of Environment and Society, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jiajia Liu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, School of Life Sciences, Fudan University, Shanghai, China. .,Institute of Eco-Chongming, Shanghai, China.
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15
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Lu CW, Huang ST, Cheng SJ, Lin CT, Hsu YC, Yao CT, Dong F, Hung CM, Kuo HC. Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Mol Ecol 2023; 32:2234-2251. [PMID: 36748940 DOI: 10.1111/mec.16875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/17/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023]
Abstract
Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.
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Affiliation(s)
- Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Ting Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shun-Jen Cheng
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Tau Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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16
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Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS. Int J Mol Sci 2023; 24:ijms24021700. [PMID: 36675215 PMCID: PMC9863576 DOI: 10.3390/ijms24021700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/27/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar 'Chinese Spring' detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci.
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17
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Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
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18
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Ashraf B, Hunter DC, Bérénos C, Ellis PA, Johnston SE, Pilkington JG, Pemberton JM, Slate J. Genomic prediction in the wild: A case study in Soay sheep. Mol Ecol 2022; 31:6541-6555. [PMID: 34719074 DOI: 10.1111/mec.16262] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/13/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
Genomic prediction, the technique whereby an individual's genetic component of their phenotype is estimated from its genome, has revolutionised animal and plant breeding and medical genetics. However, despite being first introduced nearly two decades ago, it has hardly been adopted by the evolutionary genetics community studying wild organisms. Here, genomic prediction is performed on eight traits in a wild population of Soay sheep. The population has been the focus of a >30 year evolutionary ecology study and there is already considerable understanding of the genetic architecture of the focal Mendelian and quantitative traits. We show that the accuracy of genomic prediction is high for all traits, but especially those with loci of large effect segregating. Five different methods are compared, and the two methods that can accommodate zero-effect and large-effect loci in the same model tend to perform best. If the accuracy of genomic prediction is similar in other wild populations, then there is a real opportunity for pedigree-free molecular quantitative genetics research to be enabled in many more wild populations; currently the literature is dominated by studies that have required decades of field data collection to generate sufficiently deep pedigrees. Finally, some of the potential applications of genomic prediction in wild populations are discussed.
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Affiliation(s)
- Bilal Ashraf
- School of Biosciences, University of Sheffield, Sheffield, UK.,Department of Anthropology, Durham University, Durham, UK
| | - Darren C Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK.,School of Biology, University of St Andrews, St Andrews, UK
| | - Camillo Bérénos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Philip A Ellis
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Jill G Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | | | - Jon Slate
- School of Biosciences, University of Sheffield, Sheffield, UK
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19
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Sheldon BC, Kruuk LEB, Alberts SC. The expanding value of long-term studies of individuals in the wild. Nat Ecol Evol 2022; 6:1799-1801. [DOI: 10.1038/s41559-022-01940-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Pemberton JM, Kruuk LE, Clutton-Brock T. The Unusual Value of Long-Term Studies of Individuals: The Example of the Isle of Rum Red Deer Project. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022. [DOI: 10.1146/annurev-ecolsys-012722-024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Long-term studies of individuals enable incisive investigations of questions across ecology and evolution. Here, we illustrate this claim by reference to our long-term study of red deer on the Isle of Rum, Scotland. This project has established many of the characteristics of social organization, selection, and population ecology typical of large, polygynous, seasonally breeding mammals, with wider implications for our understanding of sexual selection and the evolution of sex differences, as well as for their population dynamics and population management. As molecular genetic techniques have developed, the project has pivoted to investigate evolutionary genetic questions, also breaking new ground in this field. With ongoing advances in genomics and statistical approaches and the development of increasingly sophisticated ways to assay new phenotypic traits, the questions that long-term studies such as the red deer study can answer become both broader and ever more sophisticated. They also offer powerful means of understanding the effects of ongoing climate change on wild populations.
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Affiliation(s)
- Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Loeske E.B. Kruuk
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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21
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Campagna L, Toews DP. The genomics of adaptation in birds. Curr Biol 2022; 32:R1173-R1186. [DOI: 10.1016/j.cub.2022.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Hüppi E, Geiger M. Fast‐paced city life? Tempo and mode of phenotypic changes in urban birds from Switzerland. Ecol Evol 2022. [DOI: 10.1002/ece3.9217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Evelyn Hüppi
- University of Zurich, Palaeontological Institute and Museum Zürich Switzerland
| | - Madeleine Geiger
- Naturmuseum St. Gallen St. Gallen Switzerland
- SWILD, Urban Ecology & Wildlife Research Zurich Switzerland
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23
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Aubry LM, Williams CT. Vertebrate Phenological Plasticity: from Molecular Mechanisms to Ecological and Evolutionary Implications. Integr Comp Biol 2022; 62:958-971. [PMID: 35867980 DOI: 10.1093/icb/icac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/28/2022] [Accepted: 04/04/2022] [Indexed: 11/12/2022] Open
Abstract
Seasonal variation in the availability of essential resources is one of the most important drivers of natural selection on the phasing and duration of annually recurring life-cycle events. Shifts in seasonal timing are among the most commonly reported responses to climate change and the capacity of organisms to adjust their timing, either through phenotypic plasticity or evolution, is a critical component of resilience. Despite growing interest in documenting and forecasting the impacts of climate change on phenology, our ability to predict how individuals, populations, and species might alter their seasonal timing in response to their changing environments is constrained by limited knowledge regarding the cues animals use to adjust timing, the endogenous genetic and molecular mechanisms that transduce cues into neural and endocrine signals, and the inherent capacity of animals to alter their timing and phasing within annual cycles. Further, the fitness consequences of phenological responses are often due to biotic interactions within and across trophic levels, rather than being simple outcomes of responses to changes in the abiotic environment. Here, we review the current state of knowledge regarding the mechanisms that control seasonal timing in vertebrates, as well as the ecological and evolutionary consequences of individual, population, and species-level variation in phenological responsiveness. Understanding the causes and consequences of climate-driven phenological shifts requires combining ecological, evolutionary, and mechanistic approaches at individual, populational, and community scales. Thus, to make progress in forecasting phenological responses and demographic consequences, we need to further develop interdisciplinary networks focused on climate change science.
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Affiliation(s)
- Lise M Aubry
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, 1474 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Cory T Williams
- Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA
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24
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Ali M, Danting S, Wang J, Sadiq H, Rasheed A, He Z, Li H. Genetic Diversity and Selection Signatures in Synthetic-Derived Wheats and Modern Spring Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:877496. [PMID: 35903232 PMCID: PMC9315363 DOI: 10.3389/fpls.2022.877496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
Synthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.
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Affiliation(s)
- Mohsin Ali
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, China
| | - Shan Danting
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, China
| | - Jiankang Wang
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hafsa Sadiq
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Awais Rasheed
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Huihui Li
- Institute of Crop Sciences and CIMMYT China Office, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya, China
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25
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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26
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Clark JD, Benham PM, Maldonado JE, Luther DA, Lim HC. Maintenance of local adaptation despite gene flow in a coastal songbird. Evolution 2022; 76:1481-1494. [PMID: 35700208 PMCID: PMC9545442 DOI: 10.1111/evo.14538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 01/22/2023]
Abstract
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
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Affiliation(s)
- Jonathan D. Clark
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Current Address: Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire03824
| | - Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Jesus E. Maldonado
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013
| | - David A. Luther
- Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
| | - Haw Chuan Lim
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013,Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
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27
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Yang J, Liang B, Zhang Y, Liu Y, Wang S, Yang Q, Geng X, Liu S, Wu Y, Zhu Y, Lin T. Genome-wide association study of eigenvectors provides genetic insights into selective breeding for tomato metabolites. BMC Biol 2022; 20:120. [PMID: 35606872 PMCID: PMC9128223 DOI: 10.1186/s12915-022-01327-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/10/2022] [Indexed: 01/05/2023] Open
Abstract
Background Long-term domestication and intensive breeding of crop plants aim to establish traits desirable for human needs, and characteristics related to yield, disease resistance, and postharvest storage have traditionally received considerable attention. These processes have led also to negative consequences, as is the case of loss of variants controlling fruit quality, for instance in tomato. Tomato fruit quality is directly associated to metabolite content profiles; however, a full understanding of the genetics affecting metabolite content during tomato domestication and improvement has not been reached due to limitations of the single detection methods previously employed. Here, we aim to reach a broad understanding of changes in metabolite content using a genome-wide association study (GWAS) with eigenvector decomposition (EigenGWAS) on tomato accessions. Results An EigenGWAS was performed on 331 tomato accessions using the first eigenvector generated from the genomic data as a “phenotype” to understand the changes in fruit metabolite content during breeding. Two independent gene sets were identified that affected fruit metabolites during domestication and improvement in consumer-preferred tomatoes. Furthermore, 57 candidate genes related to polyphenol and polyamine biosynthesis were discovered, and a major candidate gene chlorogenate: glucarate caffeoyltransferase (SlCGT) was identified, which affected the quality and diseases resistance of tomato fruit, revealing the domestication mechanism of polyphenols. Conclusions We identified gene sets that contributed to consumer liking during domestication and improvement of tomato. Our study reports novel evidence of selective sweeps and key metabolites controlled by multiple genes, increasing our understanding of the mechanisms of metabolites variation during those processes. It also supports a polygenic selection model for the application of tomato breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01327-x.
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28
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Hunter DC, Ashraf B, Bérénos C, Ellis PA, Johnston SE, Wilson AJ, Pilkington JG, Pemberton JM, Slate J. Using genomic prediction to detect microevolutionary change of a quantitative trait. Proc Biol Sci 2022; 289:20220330. [PMID: 35538786 PMCID: PMC9091855 DOI: 10.1098/rspb.2022.0330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/12/2022] [Indexed: 12/31/2022] Open
Abstract
Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply a genomic prediction approach to estimate breeding values of adult weight in a 35-year dataset of Soay sheep (Ovis aries). Comparisons are made with a traditional pedigree-based approach. During the study period, adult body weight decreased, but the underlying genetic component of body weight increased, at a rate that is unlikely to be attributable to genetic drift. Thus cryptic microevolution of greater adult body weight has probably occurred. Genomic and pedigree-based approaches gave largely consistent results. Thus, using genomic prediction to study microevolution in wild populations can remove the requirement for pedigree data, potentially opening up new study systems for similar research.
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Affiliation(s)
- D. C. Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- School of Biology, University of St Andrews, St Andrews KY16 9ST, UK
| | - B. Ashraf
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Anthropology, Durham University, Durham DH1 3LE, UK
| | - C. Bérénos
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - P. A. Ellis
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - S. E. Johnston
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - A. J. Wilson
- Centre of Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, UK
| | - J. G. Pilkington
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J. M. Pemberton
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - J. Slate
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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29
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Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
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Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
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30
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Dunn RR, Burger JR, Carlen EJ, Koltz AM, Light JE, Martin RA, Munshi-South J, Nichols LM, Vargo EL, Yitbarek S, Zhao Y, Cibrián-Jaramillo A. A Theory of City Biogeography and the Origin of Urban Species. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.761449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many of the choices humans make with regard to infrastructure, urban planning and other phenomena have impacts that will last thousands of years. This can readily be seen in modern cities in which contemporary streets run along street grids that were laid out thousands of years prior or even in which ancient viaducts still play a role. However, rarely do evolutionary biologists explicitly consider the future of life likely to be associated with the decisions we are making today. Here, we consider the evolutionary future of species in cities with a focus on the origin of lineages and species. We do so by adjusting evolutionary predictions from the theory of island biogeography so as to correspond to the unique features of cities as islands. Specifically, the species endemic to cities tend to be associated with the gray habitats in cities. Those habitats tend to be dominated by human bodies, pet bodies and stored food. It is among such species where the origin of new lineages is most likely, although most research on evolution in cities has focused on green habitats. We conclude by considering a range of scenarios for the far future and their implications for the origin of lineages and species.
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31
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Goumas M, Boogert NJ, Kelley LA, Holding T. Predator or provider? How wild animals respond to mixed messages from humans. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211742. [PMID: 35308627 PMCID: PMC8924750 DOI: 10.1098/rsos.211742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 02/22/2022] [Indexed: 05/03/2023]
Abstract
Wild animals encounter humans on a regular basis, but humans vary widely in their behaviour: whereas many people ignore wild animals, some people present a threat, while others encourage animals' presence through feeding. Humans thus send mixed messages to which animals must respond appropriately to be successful. Some species appear to circumvent this problem by discriminating among and/or socially learning about humans, but it is not clear whether such learning strategies are actually beneficial in most cases. Using an individual-based model, we consider how learning rate, individual recognition (IR) of humans, and social learning (SL) affect wild animals' ability to reach an optimal avoidance strategy when foraging in areas frequented by humans. We show that 'true' IR of humans could be costly. We also find that a fast learning rate, while useful when human populations are homogeneous or highly dangerous, can cause unwarranted avoidance in other scenarios if animals generalize. SL reduces this problem by allowing conspecifics to observe benign interactions with humans. SL and a fast learning rate also improve the viability of IR. These results provide an insight into how wild animals may be affected by, and how they may cope with, contrasting human behaviour.
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Affiliation(s)
- Madeleine Goumas
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Treliever Road, Penryn TR10 9FE, United Kingdom
| | - Neeltje J. Boogert
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Treliever Road, Penryn TR10 9FE, United Kingdom
| | - Laura A. Kelley
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Treliever Road, Penryn TR10 9FE, United Kingdom
| | - Thomas Holding
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
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32
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Molecular parallelism in signaling function across different sexually selected ornaments in a warbler. Proc Natl Acad Sci U S A 2022; 119:2120482119. [PMID: 35165176 PMCID: PMC8872772 DOI: 10.1073/pnas.2120482119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Extravagant ornaments are thought to signal male quality to females choosing mates, but the evidence linking ornament size to male quality is controversial, particularly in cases in which females prefer different ornaments in different populations. Here, we use whole-genome sequencing and transcriptomics to determine the genetic basis of ornament size in two populations of a widespread warbler, the common yellowthroat (Geothlypis trichas). Within a single subspecies, females in a Wisconsin population prefer males with larger black masks as mates, while females in a New York population prefer males with larger yellow bibs. Despite being produced by different pigments in different patches on the body, the size of the ornament preferred by females in each population was linked to numerous genes that function in many of the same core aspects of male quality (e.g., immunity and oxidative balance). These relationships confirm recent hypotheses linking the signaling function of ornaments to male quality. Furthermore, the parallelism in signaling function provides the flexibility for different types of ornaments to be used as signals of similar aspects of male quality. This could facilitate switches in female preference for different ornaments, a potentially important step in the early stages of divergence among populations.
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33
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Lever D, Rush LV, Thorogood R, Gotanda KM. Darwin's small and medium ground finches might have taste preferences, but not for human foods. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211198. [PMID: 35116148 PMCID: PMC8790341 DOI: 10.1098/rsos.211198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Urbanization is rapidly changing ecological niches. On the inhabited Galapagos Islands, Darwin's finches consume human-introduced foods preferentially; however, it remains unclear why. Here, we presented pastry with flavour profiles typical of human foods (oily, salty and sweet) to small ground finches (Geospiza fuliginosa) and medium ground finches (Geospiza fortis) to test if latent taste preferences might drive the selection of human foods. If human food flavours were consumed more than a neutral or bitter control only at sites with human foods, then we predicted tastes were acquired after urbanization; however, if no site differences were found then this would indicate latent taste preferences. Contrary to both predictions, we found little evidence that human food flavours were preferred compared with control flavours at any site. Instead, finches showed a weak aversion to oily foods, but only at remote (no human foods present) sites. This was further supported by behavioural responses, with beak-wiping occurring more often at remote sites after finches tasted flavours associated with human foods. Our results suggest, therefore, that while Darwin's finches regularly exposed to human foods might have acquired a tolerance to human food flavours, latent taste preferences are unlikely to have played a major role in their dietary response to increased urbanization.
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Affiliation(s)
- D. Lever
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - L. V. Rush
- Department of Geology, Laurentian University, 935 Ramsey Lake Rd, Sudbury, Ontario P3E 2C6, Canada
| | - R. Thorogood
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- Helsinki Institute of Life Science (HiLIFE), Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
- Research Program in Organismal and Evolutionary Biology, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - K. M. Gotanda
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
- Départment de Biologie, Université de Sherbrooke, 2500, boul de l'Université, Sherbrooke, Québec J1K 2R1, Canada
- Department of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St Catharine's, Ontario L2S 3A1, Canada
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34
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Boer EF, Maclary ET, Shapiro MD. Complex genetic architecture of three-dimensional craniofacial shape variation in domestic pigeons. Evol Dev 2021; 23:477-495. [PMID: 34914861 PMCID: PMC9119316 DOI: 10.1111/ede.12395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 10/28/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
Deciphering the genetic basis of vertebrate craniofacial variation is a longstanding biological problem with broad implications in evolution, development, and human pathology. One of the most stunning examples of craniofacial diversification is the adaptive radiation of birds, in which the beak serves essential roles in virtually every aspect of their life histories. The domestic pigeon (Columba livia) provides an exceptional opportunity to study the genetic underpinnings of craniofacial variation because of its unique balance of experimental accessibility and extraordinary phenotypic diversity within a single species. We used traditional and geometric morphometrics to quantify craniofacial variation in an F2 laboratory cross derived from the straight-beaked Pomeranian Pouter and curved-beak Scandaroon pigeon breeds. Using a combination of genome-wide quantitative trait locus scans and multi-locus modeling, we identified a set of genetic loci associated with complex shape variation in the craniofacial skeleton, including beak shape, braincase shape, and mandible shape. Some of these loci control coordinated changes between different structures, while others explain variation in the size and shape of specific skull and jaw regions. We find that in domestic pigeons, a complex blend of both independent and coupled genetic effects underlie three-dimensional craniofacial morphology.
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Affiliation(s)
- Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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35
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Christmas MJ, Jones JC, Olsson A, Wallerman O, Bunikis I, Kierczak M, Whitley KM, Sullivan I, Geib JC, Miller-Struttmann NE, Webster MT. A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component. Mol Ecol 2021; 31:1111-1127. [PMID: 34837435 DOI: 10.1111/mec.16291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 11/16/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022]
Abstract
Over the last six decades, populations of the bumblebees Bombus sylvicola and Bombus balteatus in Colorado have experienced decreases in tongue length, a trait important for plant-pollinator mutualisms. It has been hypothesized that this observation reflects selection resulting from shifts in floral composition under climate change. Here we used morphometrics and population genomics to determine whether morphological change is ongoing, investigate the genetic basis of morphological variation, and analyse population structure in these populations. We generated a genome assembly of B. balteatus. We then analysed whole-genome sequencing data and morphometric measurements of 580 samples of both species from seven high-altitude localities. Out of 281 samples originally identified as B. sylvicola, 67 formed a separate genetic cluster comprising a newly-discovered cryptic species ("incognitus"). However, an absence of genetic structure within species suggests that gene flow is common between mountains. We found a significant decrease in tongue length between bees collected between 2012-2014 and in 2017, indicating that morphological shifts are ongoing. We did not discover any genetic associations with tongue length, but a SNP related to production of a proteolytic digestive enzyme was implicated in body size variation. We identified evidence of covariance between kinship and both tongue length and body size, which is suggestive of a genetic component of these traits, although it is possible that shared environmental effects between colonies are responsible. Our results provide evidence for ongoing modification of a morphological trait important for pollination and indicate that this trait probably has a complex genetic and environmental basis.
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Affiliation(s)
- Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Julia C Jones
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kaitlyn M Whitley
- Department of Biology, Appalachian State University, Boone, North Carolina, USA.,U.S. Department of Agriculture, Agriculture Research Service, Charleston, South Carolina, USA
| | - Isabel Sullivan
- Department of Biology, Appalachian State University, Boone, North Carolina, USA.,Marine Estuarine Environmental Sciences, University of Maryland, College Park, Maryland, USA
| | - Jennifer C Geib
- Department of Biology, Appalachian State University, Boone, North Carolina, USA
| | | | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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36
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Boer EF, Van Hollebeke HF, Maclary ET, Holt C, Yandell M, Shapiro MD. A ROR2 coding variant is associated with craniofacial variation in domestic pigeons. Curr Biol 2021; 31:5069-5076.e5. [PMID: 34551284 PMCID: PMC8612976 DOI: 10.1016/j.cub.2021.08.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/01/2021] [Accepted: 08/30/2021] [Indexed: 11/23/2022]
Abstract
Vertebrate craniofacial morphogenesis is a highly orchestrated process that is directed by evolutionarily conserved developmental pathways.1,2 Within species, canalized development typically produces modest morphological variation. However, as a result of millennia of artificial selection, the domestic pigeon displays radical craniofacial variation within a single species. One of the most striking cases of pigeon craniofacial variation is the short-beak phenotype, which has been selected in numerous breeds. Classical genetic experiments suggest that pigeon beak length is regulated by a small number of genetic factors, one of which is sex linked (Ku2 locus).3-5 However, the genetic underpinnings of pigeon craniofacial variation remain unknown. Using geometric morphometrics and quantitative trait locus (QTL) mapping on an F2 intercross between a short-beaked Old German Owl (OGO) and a medium-beaked Racing Homer (RH), we identified a single Z chromosome locus that explains a majority of the variation in beak morphology in the F2 population. Complementary comparative genomic analyses revealed that the same locus is strongly differentiated between breeds with short and medium beaks. Within the Ku2 locus, we identified an amino acid substitution in the non-canonical Wnt receptor ROR2 as a putative regulator of pigeon beak length. The non-canonical Wnt pathway serves critical roles in vertebrate neural crest cell migration and craniofacial morphogenesis.6,7 In humans, ROR2 mutations cause Robinow syndrome, a congenital disorder characterized by skeletal abnormalities, including a widened and shortened facial skeleton.8,9 Our results illustrate how the extraordinary craniofacial variation among pigeons can reveal genetic regulators of vertebrate craniofacial diversity.
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Affiliation(s)
- Elena F Boer
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Emily T Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Carson Holt
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA
| | - Michael D Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA.
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Bravo GA, Schmitt CJ, Edwards SV. What Have We Learned from the First 500 Avian Genomes? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-085928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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38
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Hanif U, Alipour H, Gul A, Jing L, Darvishzadeh R, Amir R, Munir F, Ilyas MK, Ghafoor A, Siddiqui SU, St Amand P, Bernado A, Bai G, Sonder K, Rasheed A, He Z, Li H. Characterization of the genetic basis of local adaptation of wheat landraces from Iran and Pakistan using genome-wide association study. THE PLANT GENOME 2021; 14:e20096. [PMID: 34275212 DOI: 10.1002/tpg2.20096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/31/2021] [Indexed: 05/21/2023]
Abstract
Characterization of genomic regions underlying adaptation of landraces can reveal a quantitative genetics framework for local wheat (Triticum aestivum L.) adaptability. A collection of 512 wheat landraces from the eastern edge of the Fertile Crescent in Iran and Pakistan were genotyped using genome-wide single nucleotide polymorphism markers generated by genotyping-by-sequencing. The minor allele frequency (MAF) and the heterozygosity (H) of Pakistani wheat landraces (MAF = 0.19, H = 0.008) were slightly higher than the Iranian wheat landraces (MAF = 0.17, H = 0.005), indicating that Pakistani landraces were slightly more genetically diverse. Population structure analysis clearly separated the Pakistani landraces from Iranian landraces, which indicates two separate adaptability trajectories. The large-scale agro-climatic data of seven variables were quite dissimilar between Iran and Pakistan as revealed by the correlation coefficients. Genome-wide association study identified 91 and 58 loci using agroclimatic data, which likely underpin local adaptability of the wheat landraces from Iran and Pakistan, respectively. Selective sweep analysis identified significant hits on chromosomes 4A, 4B, 6B, 7B, 2D, and 6D, which were colocalized with the loci associated with local adaptability and with some known genes related to flowering time and grain size. This study provides insight into the genetic diversity with emphasis on the genetic architecture of loci involved in adaptation to local environments, which has breeding implications.
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Affiliation(s)
- Uzma Hanif
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Hadi Alipour
- Dep. of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia Univ., Urmia, Iran
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Li Jing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
| | - Reza Darvishzadeh
- Dep. of Plant Production and Genetics, Faculty of Agriculture and Natural Resources, Urmia Univ., Urmia, Iran
| | - Rabia Amir
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Faiza Munir
- Atta-ur-Rahman School of Applied Biosciences, National Univ. of Sciences and Technology, Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Abdul Ghafoor
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Sadar Uddin Siddiqui
- Plant Genetic Resource Program, Bioresource Conservation Institute, National Agricultural Research Center, Islamabad, 44000, Pakistan
| | - Paul St Amand
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Amy Bernado
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Guihua Bai
- USDA Hard Winter Wheat Genetics Research Unit, Manhattan, KS, 66506, USA
| | - Kai Sonder
- International Wheat and Maize Improvement Center (CIMMYT), Texcoco, Mexico
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
- Dep. of Plant Sciences, Quaid-i-Azam Univ., Islamabad, 45320, Pakistan
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), & CIMMYT-China office, 12 Zhongguancun South St., Beijing, 100081, China
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39
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Gompert Z, Feder JL, Nosil P. Natural selection drives genome-wide evolution via chance genetic associations. Mol Ecol 2021; 31:467-481. [PMID: 34704650 DOI: 10.1111/mec.16247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022]
Abstract
Understanding selection's impact on the genome is a major theme in biology. Functionally neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here, we use field experiments and genomic data in stick insects, deer mice and stickleback fish to show that widespread statistical associations with genes known to affect fitness cause many genetic loci across the genome to be impacted indirectly by selection. This includes regions physically distant from those directly under selection. Then, focusing on the stick insect system, we show that statistical associations between SNPs and other unknown, causal variants result in additional indirect selection in general and specifically within genomic regions of physically linked loci. This widespread indirect selection necessarily makes aspects of evolution more predictable. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations. This process has implications for the application of evolutionary principles in basic and applied science.
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Affiliation(s)
- Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah, USA.,Ecology Center, Utah State University, Logan, Utah, USA
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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40
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Ryding S, Klaassen M, Tattersall GJ, Gardner JL, Symonds MRE. Shape-shifting: changing animal morphologies as a response to climatic warming. Trends Ecol Evol 2021; 36:1036-1048. [PMID: 34507845 DOI: 10.1016/j.tree.2021.07.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/19/2022]
Abstract
Many animal appendages, such as avian beaks and mammalian ears, can be used to dissipate excess body heat. Allen's rule, wherein animals in warmer climates have larger appendages to facilitate more efficient heat exchange, reflects this. We find that there is widespread evidence of 'shape-shifting' (changes in appendage size) in endotherms in response to climate change and its associated climatic warming. We re-examine studies of morphological change over time within a thermoregulatory context, finding evidence that temperature can be a strong predictor of morphological change independently of, or combined with, other environmental changes. Last, we discuss how Allen's rule, the degree of temperature change, and other ecological factors facilitate morphological change and make predictions about what animals will show shape-shifting.
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Affiliation(s)
- Sara Ryding
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia.
| | - Marcel Klaassen
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
| | - Glenn J Tattersall
- Department of Biological Sciences, Brock University, 500 Glenridge Avenue, Saint Catharines, Ontario L2S 3A1, Canada
| | - Janet L Gardner
- Division of Ecology & Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Matthew R E Symonds
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Burwood, Victoria 3125, Australia
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41
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Papadopulos AST, Helmstetter AJ, Osborne OG, Comeault AA, Wood DP, Straw EA, Mason L, Fay MF, Parker J, Dunning LT, Foote AD, Smith RJ, Lighten J. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Mol Biol Evol 2021; 38:3724-3736. [PMID: 33950261 PMCID: PMC8382892 DOI: 10.1093/molbev/msab141] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.
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Affiliation(s)
- Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Andrew J Helmstetter
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- FRB-CESAB, Institut Bouisson Bertrand, Rue de l'École de Médecine, Montpellier, France
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Aaron A Comeault
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Daniel P Wood
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Edward A Straw
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School for Life Sciences and the Environment, Royal Holloway University of London, Egham, United Kingdom
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Joe Parker
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Biofilms Innovation Centre, Department of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Department of Natural History, Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Rhian J Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jackie Lighten
- Biosciences, University of Exeter, Exeter, United Kingdom
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42
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McGaugh SE, Lorenz AJ, Flagel LE. The utility of genomic prediction models in evolutionary genetics. Proc Biol Sci 2021; 288:20210693. [PMID: 34344180 PMCID: PMC8334854 DOI: 10.1098/rspb.2021.0693] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 07/15/2021] [Indexed: 12/25/2022] Open
Abstract
Variation in complex traits is the result of contributions from many loci of small effect. Based on this principle, genomic prediction methods are used to make predictions of breeding value for an individual using genome-wide molecular markers. In breeding, genomic prediction models have been used in plant and animal breeding for almost two decades to increase rates of genetic improvement and reduce the length of artificial selection experiments. However, evolutionary genomics studies have been slow to incorporate this technique to select individuals for breeding in a conservation context or to learn more about the genetic architecture of traits, the genetic value of missing individuals or microevolution of breeding values. Here, we outline the utility of genomic prediction and provide an overview of the methodology. We highlight opportunities to apply genomic prediction in evolutionary genetics of wild populations and the best practices when using these methods on field-collected phenotypes.
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Affiliation(s)
- Suzanne E. McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Aaron J. Lorenz
- Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN 55108, USA
| | - Lex E. Flagel
- Plant and Microbial Biology, University of Minnesota, 140 Gortner Lab, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
- Bayer Crop Science, 700 W Chesterfield Parkway, Chesterfield, MO 63017, USA
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43
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Phenotypic variation in a neotropical understory bird driven by environmental change in an urbanizing Amazonian landscape. Oecologia 2021; 196:763-779. [PMID: 34259906 DOI: 10.1007/s00442-021-04976-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 06/19/2021] [Indexed: 10/20/2022]
Abstract
Environmental change through habitat fragmentation and urbanization drives biodiversity loss in the Neotropics at an alarming rate. Some individuals and species confined to habitat fragments may develop phenotypic adjustments that allow populations to persist, even in landscapes made harsh by human activities. Behavioral and morphological adjustments may enhance a population's ability to cope with anthropogenic hazards. We examined potential differences in the behavioral and morphological phenotype of populations of the neotropical Wedge-billed Woodcreeper (Glyphorynchus spirurus)-an understory forest specialist insectivorous bird-between populations from urban fragmented forests and continuous preserved forests. We evaluated exploratory behavior and morphological traits using generalized linear models and linear discriminant analysis to quantify phenotypical differences among populations. We used failure time analysis to compare latency to explore and move during exploration in a Novel Environment Test (NET). Our analyses detected differences in certain movement behaviors (latencies to move during NET), indicating that individuals from fragmented forests are slow explorers in relation to individuals from the continuous forest. We also found shorter tarsi and tails in the fragmented forest population which were attributed to an overall reduction in body size in these populations. Our results suggest that environmental change driven by fragmentation in an urban landscape is causing population differentiation, but we cannot ascribe observed variations to evolutionary processes only, as the differences observed may be explained by other processes too. However, we suggest that phenotypic differences may be aiding this small understory forest specialist to persist in an urban fragmented landscape.
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44
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Van Doren BM, Conway GJ, Phillips RJ, Evans GC, Roberts GCM, Liedvogel M, Sheldon BC. Human activity shapes the wintering ecology of a migratory bird. GLOBAL CHANGE BIOLOGY 2021; 27:2715-2727. [PMID: 33849083 DOI: 10.1111/gcb.15597] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Human behavior profoundly affects the natural world. Migratory birds are particularly susceptible to adverse effects of human activities because the global networks of ecosystems on which birds rely are undergoing rapid change. In spite of these challenges, the blackcap (Sylvia atricapilla) is a thriving migratory species. Its recent establishment of high-latitude wintering areas in Britain and Ireland has been linked to climate change and backyard bird feeding, exemplifying the interaction between human activity and migrant ecology. To understand how anthropogenic influences shape avian movements and ecology, we marked 623 wintering blackcaps at 59 sites across Britain and Ireland and compiled a dataset of 9929 encounters. We investigated visitation behavior at garden feeding sites, inter-annual site fidelity, and movements within and across seasons. We analyzed migration tracks from 25 geolocators fitted to a subset of individuals to understand how garden behavior may impact subsequent migration and breeding. We found that blackcaps wintering in Britain and Ireland showed high site fidelity and low transience among wintering sites, in contrast to the itinerant movements characteristic of blackcaps wintering in their traditional winter range. First-winter birds showed lower site fidelity and a greater likelihood of transience than adults. Adults that frequented gardens had better body condition, smaller fat stores, longer bills, and rounder wingtips. However, blackcaps did not exclusively feed in gardens; visits were linked to harsher weather. Individuals generally stayed at garden sites until immediately before spring departure. Our results suggest that supplementary feeding is modifying blackcap winter ecology and driving morphological evolution. Supplemental feeding may have multifaceted benefits on winter survival, and these positive effects may carry over to migration and subsequent breeding. Overall, the high individual variability in blackcap movement and foraging ecology, and the flexibility it imparts, may have allowed this species to flourish during rapid environmental change.
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Affiliation(s)
- Benjamin M Van Doren
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | | | | | | | | | - Miriam Liedvogel
- Max Planck Institute for Evolutionary Biology, MPRG Behavioural Genomics, Plön, Germany
- Institute of Avian Research "Vogelwarte Helgoland", Wilhelmshaven, Germany
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
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45
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Shutt JD, Trivedi UH, Nicholls JA. Faecal metabarcoding reveals pervasive long-distance impacts of garden bird feeding. Proc Biol Sci 2021; 288:20210480. [PMID: 34034514 PMCID: PMC8150026 DOI: 10.1098/rspb.2021.0480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Supplementary feeding of wildlife is widespread, being undertaken by more than half of households in many countries. However, the impact that these supplemental resources have is unclear, with impacts largely considered to be restricted to urban ecosystems. We reveal the pervasiveness of supplementary foodstuffs in the diet of a wild bird using metabarcoding of blue tit (Cyanistes caeruleus) faeces collected in early spring from a 220 km transect in Scotland with a large urbanization gradient. Supplementary foodstuffs were present in the majority of samples, with peanut (Arachis hypogaea) the single commonest (either natural or supplementary) dietary item. Consumption rates exhibited a distance decay from human habitation but remained high at several hundred metres from the nearest household and continued to our study limit of 1.4 km distant. Supplementary food consumption was associated with a near quadrupling of blue tit breeding density and a 5-day advancement of breeding phenology. We show that woodland bird species using supplementary food have increasing UK population trends, while species that do not, and/or are outcompeted by blue tits, are likely to be declining. We suggest that the impacts of supplementary feeding are larger and more spatially extensive than currently appreciated and could be disrupting population and ecosystem dynamics.
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Affiliation(s)
- Jack D. Shutt
- Department of Natural Sciences, Manchester Metropolitan University, Manchester M1 5GD, UK
- Institute of Evolutionary Biology, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Urmi H. Trivedi
- Edinburgh Genomics, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - James A. Nicholls
- Institute of Evolutionary Biology, University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
- Australian National Insect Collection, CSIRO, Acton, Australian Capital Territory 2601, Australia
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46
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Salmón P, Jacobs A, Ahrén D, Biard C, Dingemanse NJ, Dominoni DM, Helm B, Lundberg M, Senar JC, Sprau P, Visser ME, Isaksson C. Continent-wide genomic signatures of adaptation to urbanisation in a songbird across Europe. Nat Commun 2021; 12:2983. [PMID: 34016968 PMCID: PMC8137928 DOI: 10.1038/s41467-021-23027-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 04/01/2021] [Indexed: 02/03/2023] Open
Abstract
Urbanisation is increasing worldwide, and there is now ample evidence of phenotypic changes in wild organisms in response to this novel environment. Yet, the genetic changes and genomic architecture underlying these adaptations are poorly understood. Here, we genotype 192 great tits (Parus major) from nine European cities, each paired with an adjacent rural site, to address this major knowledge gap in our understanding of wildlife urban adaptation. We find that a combination of polygenic allele frequency shifts and recurrent selective sweeps are associated with the adaptation of great tits to urban environments. While haplotypes under selection are rarely shared across urban populations, selective sweeps occur within the same genes, mostly linked to neural function and development. Collectively, we show that urban adaptation in a widespread songbird occurs through unique and shared selective sweeps in a core-set of behaviour-linked genes.
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Affiliation(s)
- Pablo Salmón
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden ,grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Arne Jacobs
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Dag Ahrén
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Clotilde Biard
- grid.462350.6Sorbonne Université, UPEC, Paris 7, CNRS, INRA, IRD, Institut d’Écologie et des Sciences de l’Environnement de Paris, iEES Paris, F-75005 Paris, France
| | - Niels J. Dingemanse
- grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Davide M. Dominoni
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Barbara Helm
- grid.8756.c0000 0001 2193 314XInstitute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK ,grid.4830.f0000 0004 0407 1981Present Address: GELIFES - Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Max Lundberg
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
| | - Juan Carlos Senar
- grid.507605.10000 0001 1958 5537Museu de Ciències Naturals de Barcelona, Barcelona, Spain
| | - Philipp Sprau
- grid.5252.00000 0004 1936 973XDepartment of Biology, Ludwig Maximilians University Munich, Munich, Germany
| | - Marcel E. Visser
- grid.418375.c0000 0001 1013 0288Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Caroline Isaksson
- grid.4514.40000 0001 0930 2361Department of Biology, Lund University, Lund, Sweden
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47
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Sendell-Price AT, Ruegg KC, Robertson BC, Clegg SM. An island-hopping bird reveals how founder events shape genome-wide divergence. Mol Ecol 2021; 30:2495-2510. [PMID: 33826187 DOI: 10.1111/mec.15898] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
When populations colonize new areas, both strong selection and strong drift can be experienced due to novel environments and small founding populations, respectively. Empirical studies have predominantly focused on the phenotype when assessing the role of selection, and limited neutral-loci when assessing founder-induced loss of diversity. Consequently, the extent to which processes interact to influence evolutionary trajectories is difficult to assess. Genomic-level approaches provide the opportunity to simultaneously consider these processes. Here, we examine the roles of selection and drift in shaping genomic diversity and divergence in historically documented sequential island colonizations by the silvereye (Zosterops lateralis). We provide the first empirical demonstration of the rapid appearance of highly diverged genomic regions following population founding, the position of which are highly idiosyncratic. As these regions rarely contained loci putatively under selection, it is most likely that these differences arise via the stochastic nature of the founding process. However, selection is required to explain rapid evolution of larger body size in insular silvereyes. Reconciling our genomic data with these phenotypic patterns suggests there may be many genomic routes to the island phenotype, which vary across populations. Finally, we show that accelerated divergence associated with multiple founding steps is the product of genome-wide rather than localized differences, and that diversity erodes due to loss of rare alleles. However, even multiple founder events do not result in divergence and diversity levels seen in evolutionary older subspecies, and therefore do not provide a shortcut to speciation as proposed by founder-effect speciation models.
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Affiliation(s)
- Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK
| | - Kristen C Ruegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Nathan, Qld, Australia
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48
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Sengupta A, McConkey KR, Kwit C. The influence of provisioning on animal‐mediated seed dispersal. OIKOS 2021. [DOI: 10.1111/oik.08276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Asmita Sengupta
- Ashoka Trust for Research in Ecology and the Environment Bangalore Karnataka India
- National Inst. of Advanced Studies Bangalore Karnataka India
| | - Kim R. McConkey
- School of Geography, Univ. of Nottingham Malaysia Campus Semenyih Selangor Malaysia
| | - Charles Kwit
- Dept of Forestry, Wildlife and Fisheries, Univ. of Tennessee Knoxville TN USA
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49
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Qi GA, Zheng YT, Lin F, Huang X, Duan LW, You Y, Liu H, Wang Y, Xu HM, Chen GB. EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection. Mol Ecol Resour 2021; 21:1732-1744. [PMID: 33665976 DOI: 10.1111/1755-0998.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 01/17/2021] [Accepted: 02/25/2021] [Indexed: 11/30/2022]
Abstract
Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to F ST but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R-Shiny user-friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.
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Affiliation(s)
- Guo-An Qi
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuan-Ting Zheng
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Feng Lin
- Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Xin Huang
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Li-Wen Duan
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yue You
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hailan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ying Wang
- Phase I Clinical Research Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Hai-Ming Xu
- Institute of Bioinformatics and Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guo-Bo Chen
- Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China.,Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, People's Hospital of Hangzhou Medical College, Hangzhou, China
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Sepers B, Erven JAM, Gawehns F, Laine VN, van Oers K. Epigenetics and Early Life Stress: Experimental Brood Size Affects DNA Methylation in Great Tits (Parus major). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.609061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Early developmental conditions are known to have life-long effects on an individual’s behavior, physiology and fitness. In altricial birds, a majority of these conditions, such as the number of siblings and the amount of food provisioned, are controlled by the parents. This opens up the potential for parents to adjust the behavior and physiology of their offspring according to local post-natal circumstances. However, the mechanisms underlying such intergenerational regulation remain largely unknown. A mechanism often proposed to possibly explain how parental effects mediate consistent phenotypic change is DNA methylation. To investigate whether early life effects on offspring phenotypes are mediated by DNA methylation, we cross-fostered great tit (Parus major) nestlings and manipulated their brood size in a natural study population. We assessed genome-wide DNA methylation levels of CpG sites in erythrocyte DNA, using Reduced Representation Bisulfite Sequencing (RRBS). By comparing DNA methylation levels between biological siblings raised in enlarged and reduced broods and between biological siblings of control broods, we assessed which CpG sites were differentially methylated due to brood size. We found 32 differentially methylated sites (DMS) between siblings from enlarged and reduced broods, a larger number than in the comparison between siblings from control broods. A considerable number of these DMS were located in or near genes involved in development, growth, metabolism, behavior and cognition. Since the biological functions of these genes line up with previously found effects of brood size and food availability, it is likely that the nestlings in the enlarged broods suffered from nutritional stress. We therefore conclude that early life stress might directly affect epigenetic regulation of genes related to early life conditions. Future studies should link such experimentally induced DNA methylation changes to expression of phenotypic traits and assess whether these effects affect parental fitness to determine if such changes are also adaptive.
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